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By the turn of the century in 1900, most remaining Native Americans in California, like other Native Americans, had been forced, tricked, or paid to leave their ancestral lands. Some chose to live on the few California reservations that were created by the U.S. government starting in the 1890s, hand-in-hand with the U.S. government "allotment" program that took away ancestral Native American lands. Others, like Ishi's family, spent their lives hiding both from whites whom they feared would kill or capture them, and from their own people, who they viewed as having "sold out" their culture.

After the deaths and disappearances of his family members, Ishi made the decision to transmit as much of his people's culture to the new people and culture that had taken their place - the whites. Both Ishi's choice to do this and his early death from disease were seen at the time as a natural progression, or evolution, of the human race. Indians would naturally die out or become a part of white society. "Primitive" Indian language, religion, art, and technology would become something from the past to be studied or viewed in a museum, but would not be the products of living cultures. "Civilized" white society was seen as the natural end result for all humanity.

The goal of bringing Native Americans into "civilized" white society backfired as white-educated Native Americans and those increasingly familiar with white society, laws, and government started organizing and fighting alongside whites for Native American rights to land, religion, and education in the early 1900s. This struggle for Native American rights continues today, as Native Americans across the U.S. refuse to accept the stereotype that their people are "history" and not living cultures.

After another turn of a century, into 2000, Ishi again became a symbol, this time of Califonia Native American's fight to regain cultural artifacts and human remains. In many places in California, Native American religious items or artworks stolen by whites, and even human remains, are now "owned" by museums. When Ishi died in 1916, his brain was sent to the Smithsonian Institution in Washington D.C. to be studied. In 1997, a group of California Maidu Indians requested that Ishi's brain be given to them so that they could offer Ishi a proper burial in his ancestral Yahi lands. After first denying that it had Ishi's brain, the Smithsonian finally released his brain on August 8, 2000.